Hi Scott, Brian,
The SO load problem appears to be due to an outdated go-perl module.
Once that was updated to the latest version the SO loaded just fine.
This was complicated by the fact that CPAN knew about the latest
version of go-perl, and thought that it was already installed, when in
fact it was not. We scanned the whole file system for multiple copies
of go-perl and we found only one copy, and that was an older version.
I have no idea what is up with CPAN, but this problem is fixed.
Dave c.
On Thu, Jan 15, 2009 at 10:47 PM, Scott Cain <scott at scottcain.net> wrote:
> Hi Brian,
>
> I didn't get a chance to work on it--it's been a very busy week. I
> just started a test load on code from cvs and it loaded rel and SO
> without problem. It's loading GO now, but that will take a while.
> I'll give it a try on another computer with gmod 1.0.
>
> Scott
>
>
> On Fri, Jan 16, 2009 at 1:13 AM, Brian O'Connor <briandoconnor at gmail.com> wrote:
>> Hi Scott,
>>
>> Where you able to debug the ontology loading step? I was able to hack my
>> way through this but in order to build a proper 1.0 release RPM I need to
>> get the ontology to load cleanly via the build process.
>>
>> --Brian
>>
>> Scott Cain wrote:
>>>
>>> Hi Brian,
>>>
>>> I'll look at it tonight; presumably something is broken that needs
>>> fixing. I'll either get everything fixed or make you a dump.
>>>
>>> Scott
>>>
>>>
>>> On Fri, Jan 9, 2009 at 8:08 PM, Brian O'Connor <briandoconnor at gmail.com>
>>> wrote:
>>>>
>>>> Hey Scott,
>>>>
>>>> I updated to BioPerl-1.5.9_2 manually following the directions at
>>>> bioperl.org and the problem persisted. Any other ideas?
>>>>
>>>> I didn't see this on the gmod.org site but do you also distribute db
>>>> dumps
>>>> of clean databases (e.g. the default schema and base ontologies loaded)?
>>>> I
>>>> could use that to make my RPM.
>>>>
>>>> --Brian
>>>>
>>>> Scott Cain wrote:
>>>>>
>>>>> Hi Brian,
>>>>>
>>>>> Bioperl is almost certainly a problem. Nothing else jumps out at me
>>>>> at the moment; it's been a while since I've used Pg 7.4, but I don't
>>>>> think there is a problem there.
>>>>>
>>>>> Thanks for the info about the ontology links--I wasn't aware that they
>>>>> were broken.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Fri, Jan 9, 2009 at 3:50 PM, Brian O'Connor <briandoconnor at gmail.com>
>>>>> wrote:
>>>>>>
>>>>>> Hey Dave, Scott, et al.
>>>>>>
>>>>>> I'm trying to update the chado RPMs we're using in the Nelson lab from
>>>>>> version 0.003 to 1.0 of the schema (hopefully these will be ready for
>>>>>> the
>>>>>> GMOD meeting too!). So I downloaded the 1.0 schema release and
>>>>>> followed
>>>>>> the
>>>>>> install readme to build it first by hand before updating the RPM spec
>>>>>> file.
>>>>>> Everything worked OK until the ontology load step. First, two of the
>>>>>> URLs
>>>>>> referenced in load/tt2/load.conf.tt2 were out of date. It looks like
>>>>>> SourceForge is now using the following URLs:
>>>>>>
>>>>>> *
>>>>>>
>>>>>>
>>>>>> http://obo.cvs.sourceforge.net/viewvc/*checkout*/obo/obo/ontology/OBO_REL/relationship.obo
>>>>>> *
>>>>>>
>>>>>>
>>>>>> http://obo.cvs.sourceforge.net/viewvc/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo
>>>>>>
>>>>>> And this doesn't appear to be fixed in cvs HEAD e.g.:
>>>>>>
>>>>>>
>>>>>> http://gmod.cvs.sourceforge.net/viewvc/*checkout*/gmod/schema/chado/load/tt2/load.conf.tt2
>>>>>>
>>>>>> Anyway, that's a minor problem. However when I tried to do a "make
>>>>>> ontologies" step I get the following error:
>>>>>>
>>>>>> ++++++++++++++++++++++++
>>>>>> ...
>>>>>> fetching files for Sequence Ontology
>>>>>> +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>>>>>> updated
>>>>>> loading...DBD::Pg::st execute failed: ERROR: null value in column
>>>>>> "cv_id" violates not-null constraint
>>>>>> [for Statement "INSERT INTO cvterm (dbxref_id) VALUES (?)" with
>>>>>> ParamValues: 1='2033'] at /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.pm
>>>>>> line
>>>>>> 3314.
>>>>>> DBD::Pg::st execute failed: ERROR: null value in column "cv_id"
>>>>>> violates
>>>>>> not-null constraint
>>>>>> [for Statement "INSERT INTO cvterm (dbxref_id) VALUES (?)" with
>>>>>> ParamValues: 1='2033'] at /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.pm
>>>>>> line
>>>>>> 3314.
>>>>>> at /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.pm line 3324
>>>>>> DBIx::DBStag::insertrow('DBIx::DBStag=HASH(0x84ebd40)', 'cvterm',
>>>>>> 'HASH(0x8d01e70)', 'cvterm_id') called at
>>>>>> /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
>>>>>> line 1920
>>>>>> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
>>>>>> 'Data::Stag::StagImpl=ARRAY(0x8d6e3c4)') called at
>>>>>> /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
>>>>>> line 1333
>>>>>> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
>>>>>> 'Data::Stag::StagImpl=ARRAY(0x8d556f4)', 'HASH(0x8d28fa0)') called at
>>>>>> /usr/lib/perl5/site_perl/
>>>>>> .8.5/DBIx/DBStag.pm line 2077
>>>>>> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
>>>>>> 'Data::Stag::StagImpl=ARRAY(0x8d6b0dc)') called at
>>>>>> /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
>>>>>> line 1333
>>>>>> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
>>>>>> 'Data::Stag::StagImpl=ARRAY(0x8d1ad5c)') called at
>>>>>> /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
>>>>>> line 1180
>>>>>> DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x84ebd40)',
>>>>>> 'Data::Stag::StagImpl=ARRAY(0x8d38e0c)') called at
>>>>>> /usr/bin/stag-storenode.pl line 88
>>>>>> eval {...} called at /usr/bin/stag-storenode.pl line 87
>>>>>> main::store('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
>>>>>> 'Data::Stag::StagImpl=ARRAY(0x8d38e0c)') called at
>>>>>> /usr/bin/stag-storenode.pl line 137
>>>>>> main::__ANON__('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
>>>>>> 'Data::Stag::StagImpl=ARRAY(0x8d38e0c)') called at
>>>>>> /usr/lib/perl5/site_perl/5.8.5/Data/Stag/Ba
>>>>>> eHandler.pm line 572
>>>>>>
>>>>>>
>>>>>>
>>>>>> Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
>>>>>> 'cvterm_relationship') called at
>>>>>> /usr/lib/perl5/site_perl/5.8.5/Data/Stag/
>>>>>> aseHandler.pm line 720
>>>>>>
>>>>>>
>>>>>>
>>>>>> Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
>>>>>> 'HASH(0x8c810c8)') called at
>>>>>> /usr/lib/perl5/vendor_perl/5.8.5/XML/Parser
>>>>>> PerlSAX.pm line 239
>>>>>>
>>>>>>
>>>>>> XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x8c46ca0)',
>>>>>> 'XML::Parser::Expat=HASH(0x8727b64)', 'cvterm_relationship') called at
>>>>>> /usr/li
>>>>>> /perl5/vendor_perl/5.8.5/XML/Parser/PerlSAX.pm line 79
>>>>>>
>>>>>> XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x8727b64)',
>>>>>> 'cvterm_relationship') called at
>>>>>> /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread
>>>>>> multi/XML/Parser/Expat.pm line 469
>>>>>> XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x8727b64)',
>>>>>> 'FileHandle=GLOB(0x8c7e6e4)') called at
>>>>>> /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thre
>>>>>> d-multi/XML/Parser.pm line 187
>>>>>> eval {...} called at
>>>>>> /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi/XML/Parser.pm
>>>>>> line
>>>>>> 186
>>>>>> XML::Parser::parse('XML::Parser=HASH(0x87272c4)',
>>>>>> 'FileHandle=GLOB(0x8c7e6e4)') called at
>>>>>> /usr/lib/perl5/vendor_perl/5.8.5/XML/Parser/PerlSAX.pm line 14
>>>>>>
>>>>>> XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x8c46ca0)',
>>>>>> 'Handler', 'Data::Stag::BaseHandler=HASH(0x8bb2cc8)', 'Source',
>>>>>> 'HASH(0x8c1dfa0)') c
>>>>>> lled at /usr/lib/perl5/site_perl/5.8.5/Data/Stag/XMLParser.pm line 69
>>>>>>
>>>>>>
>>>>>> Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x8b31360)',
>>>>>> 'FileHandle=GLOB(0x8c7e6e4)') called at
>>>>>> /usr/lib/perl5/site_perl/5.8.5/Data/Sta
>>>>>> /BaseGenerator.pm line 476
>>>>>>
>>>>>>
>>>>>> Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x8b31360)',
>>>>>> '-file', 'tmp/song/so.oboxml', '-str', 'undef', '-fh', 'undef') called
>>>>>> at
>>>>>> /usr
>>>>>> lib/perl5/site_perl/5.8.5/Data/Stag/XMLParser.pm line 58
>>>>>>
>>>>>> Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x8b31360)',
>>>>>> '-file', 'tmp/song/so.oboxml', '-str', 'undef', '-fh', 'undef') called
>>>>>> at
>>>>>> /usr/lib
>>>>>> perl5/site_perl/5.8.5/Data/Stag/StagImpl.pm line 259
>>>>>> Data::Stag::StagImpl::parse('Data::Stag', '-format', 'undef',
>>>>>> '-file', 'tmp/song/so.oboxml', '-handler',
>>>>>> 'Data::Stag::BaseHandler=HASH(0x8bb2cc8)') call
>>>>>> d at /usr/lib/perl5/site_perl/5.8.5/Data/Stag.pm line 179
>>>>>> Data::Stag::AUTOLOAD('Data::Stag', '-format', 'undef', '-file',
>>>>>> 'tmp/song/so.oboxml', '-handler',
>>>>>> 'Data::Stag::BaseHandler=HASH(0x8bb2cc8)')
>>>>>> called at /
>>>>>> sr/bin/stag-storenode.pl line 143
>>>>>> System call 'stag-storenode.pl -d
>>>>>> 'dbi:Pg:dbname=chado_v_1.0;host=localhost;port=5432' --user gmod
>>>>>> tmp/song/so.oboxml' failed: 256
>>>>>> Died at /home/gmod/Dev/gmod-1.0/lib/Chado/Builder.pm line 315, <STDIN>
>>>>>> line
>>>>>> 1.
>>>>>> make: *** [ontologies] Error 2
>>>>>> ++++++++++++++++++++++++
>>>>>>
>>>>>> I'm using the following RPMs, see any dependency issues?
>>>>>>
>>>>>> httpd-2.0.52-32.ent.centos4
>>>>>> perl-bioperl-1.5-1.9.bp.centos4 (may need > 1.5.2?)
>>>>>> perl-go-perl-0.02-4.bp.centos4
>>>>>> postgresql-server-7.4.17-1.RHEL4.1
>>>>>> ant (missing)
>>>>>> perl-DBI-1.47-1.8.bp.centos4
>>>>>> perl-DBD-Pg-1.49-1.9.bp.centos4
>>>>>> perl-SQL-Translator-0.07-1.4.bp.centos4
>>>>>> perl-Data-Stag-0.08-1.12.bp.centos4
>>>>>> perl-XML-Parser-2.34-5
>>>>>> perl-Module-Build-0.25-1.3.bp.centos4
>>>>>> perl-Class-DBI-0.96-1.4.bp.centos4
>>>>>> perl-Class-DBI-Pg-0.08-1.7.bp.centos4
>>>>>> perl-Class-DBI-Pager-0.06-1.5.bp.centos4
>>>>>> perl-DBIx-DBStag-0.07-1.5.bp.centos4 (manually updated to
>>>>>> DBIx-DBStag-0.10
>>>>>> and dep of DBIx-DBSchema-0.36)
>>>>>> perl-XML-Simple-2.14-1.3.bp.centos4
>>>>>> perl-libwww-perl-5.805-1.12.bp.centos4
>>>>>> perl-Template-Toolkit-2.14-1.9.bp.centos4
>>>>>> perl-Log-Log4perl-0.51-1.5.bp.centos4
>>>>>>
>>>>>> Any ideas? Sorry if there's something obvious that I'm doing wrong, I
>>>>>> haven't built a DB from scratch in a long time :-)
>>>>>>
>>>>>> Thanks for the help.
>>>>>>
>>>>>> --Brian
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
>